Failed to install on MacOS Mojave 10.14.6

[darentsia]

I am using this command to install a package:

brew install rdkit --with-python3 --with-inchi --without-numpy But I'm getting this error:

Updating Homebrew...
==> Installing rdkit from rdkit/rdkit
==> Downloading https://github.com/rdkit/rdkit/archive/Release_2020_03_4.tar.gz
==> Downloading from https://codeload.github.com/rdkit/rdkit/tar.gz/Release_2020_03_4
######################################################################## 100.0%
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'numpy'
==> cmake -DRDK_INSTALL_INTREE=OFF -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_CPP_TESTS=OFF -DRDK_INSTALL_STATIC_LIBS=OFF -DBoost_NO_BOOST_CMAKE=ON -DPYTHON_EXECUTABLE='/usr/local/opt/python@3.8/bin/pytho
==> make -j4
Last 15 lines from /Users/macbook/Library/Logs/Homebrew/rdkit/02.make:
cd /tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen && /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++  -DBOOST_IOSTREAMS_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Dcoordgen_EXPORTS -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/catch/catch/single_include -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen -I/usr/local/Cellar/python@3.8/3.8.4/Frameworks/Python.framework/Versions/3.8/include/python3.8 -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/Code -isystem /usr/local/include/eigen3  -std=c++11 -stdlib=libc++ -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -stdlib=libc++ -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -fPIC   -std=gnu++11 -o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerMarchingSquares.cpp.o -c /tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen/coordgen/sketcherMinimizerMarchingSquares.cpp
[ 23%] Building CXX object External/CoordGen/CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerMolecule.cpp.o
cd /tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen && /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++  -DBOOST_IOSTREAMS_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Dcoordgen_EXPORTS -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/catch/catch/single_include -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen -I/usr/local/Cellar/python@3.8/3.8.4/Frameworks/Python.framework/Versions/3.8/include/python3.8 -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/Code -isystem /usr/local/include/eigen3  -std=c++11 -stdlib=libc++ -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -stdlib=libc++ -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -fPIC   -std=gnu++11 -o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerMolecule.cpp.o -c /tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen/coordgen/sketcherMinimizerMolecule.cpp
[ 24%] Building CXX object External/CoordGen/CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerResidue.cpp.o
cd /tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen && /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++  -DBOOST_IOSTREAMS_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Dcoordgen_EXPORTS -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/catch/catch/single_include -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen -I/usr/local/Cellar/python@3.8/3.8.4/Frameworks/Python.framework/Versions/3.8/include/python3.8 -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/Code -isystem /usr/local/include/eigen3  -std=c++11 -stdlib=libc++ -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -stdlib=libc++ -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -fPIC   -std=gnu++11 -o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerResidue.cpp.o -c /tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen/coordgen/sketcherMinimizerResidue.cpp
[ 24%] Building CXX object External/CoordGen/CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerResidueInteraction.cpp.o
cd /tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen && /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++  -DBOOST_IOSTREAMS_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Dcoordgen_EXPORTS -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/catch/catch/single_include -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen -I/usr/local/Cellar/python@3.8/3.8.4/Frameworks/Python.framework/Versions/3.8/include/python3.8 -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/Code -isystem /usr/local/include/eigen3  -std=c++11 -stdlib=libc++ -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -stdlib=libc++ -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -fPIC   -std=gnu++11 -o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerResidueInteraction.cpp.o -c /tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen/coordgen/sketcherMinimizerResidueInteraction.cpp
[ 24%] Building CXX object External/CoordGen/CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerRing.cpp.o
cd /tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen && /usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++  -DBOOST_IOSTREAMS_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -Dcoordgen_EXPORTS -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/catch/catch/single_include -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen -I/usr/local/Cellar/python@3.8/3.8.4/Frameworks/Python.framework/Versions/3.8/include/python3.8 -I/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/Code -isystem /usr/local/include/eigen3  -std=c++11 -stdlib=libc++ -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -stdlib=libc++ -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -fPIC   -std=gnu++11 -o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerRing.cpp.o -c /tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen/coordgen/sketcherMinimizerRing.cpp
[ 24%] Linking CXX shared library ../../lib/libRDKitcoordgen.dylib
cd /tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen && /usr/local/Cellar/cmake/3.17.3/bin/cmake -E cmake_link_script CMakeFiles/coordgen.dir/link.txt --verbose=1
/usr/local/Homebrew/Library/Homebrew/shims/mac/super/clang++ -std=c++11 -stdlib=libc++ -Wno-parentheses -Wno-logical-op-parentheses -Wno-format -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -stdlib=libc++ -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk -dynamiclib -Wl,-headerpad_max_install_names -compatibility_version 1.0.0 -current_version 2020.3.4 -o ../../lib/libRDKitcoordgen.2020.03.4.dylib -install_name @rpath/libRDKitcoordgen.1.dylib CMakeFiles/coordgen.dir/coordgen/CoordgenFragmentBuilder.cpp.o CMakeFiles/coordgen.dir/coordgen/CoordgenFragmenter.cpp.o CMakeFiles/coordgen.dir/coordgen/CoordgenMacrocycleBuilder.cpp.o CMakeFiles/coordgen.dir/coordgen/CoordgenMinimizer.cpp.o CMakeFiles/coordgen.dir/coordgen/CoordgenTemplates.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizer.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerAtom.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerBond.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerFragment.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerMarchingSquares.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerMolecule.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerResidue.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerResidueInteraction.cpp.o CMakeFiles/coordgen.dir/coordgen/sketcherMinimizerRing.cpp.o  -Wl,-rpath,/tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/lib ../../lib/libRDKitmaeparser.2020.03.4.dylib /usr/local/lib/libboost_system-mt.dylib /usr/local/lib/libboost_iostreams-mt.dylib /usr/local/lib/libboost_regex-mt.dylib 
cd /tmp/rdkit-20200721-99421-6als6l/rdkit-Release_2020_03_4/External/CoordGen && /usr/local/Cellar/cmake/3.17.3/bin/cmake -E cmake_symlink_library ../../lib/libRDKitcoordgen.2020.03.4.dylib ../../lib/libRDKitcoordgen.1.dylib ../../lib/libRDKitcoordgen.dylib
[ 24%] Built target coordgen
make: *** [all] Error 2

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
  https://github.com/rdkit/homebrew-rdkit/issues

Could you suggest, please, what can be done?

[UnixJunkie]

Try adding --HEAD to the CLI options.

brew install --HEAD rdkit --with-python3 --with-inchi --without-numpy 

Copy-paste the error, if any remains.

[UnixJunkie]

Maybe also, try removing the --without-numpy if problem persists.

[olgOk]

I have the same issue, e.g. the same error occurs. Neither options described above could help me to resolve the problem. Could you suggest something else?

[UnixJunkie]

Nuke the whole brew install on your computer. Reinstall it from scratch then try to install rdkit again. brew has bad reproducibility of builds (yes, it is a bad package manager). If that doesn't work, try to install rdkit using the conda recipe: https://www.rdkit.org/docs/Install.html#cross-platform-under-anaconda-python-fastest-install This is the recommended install procedure, I just hate to be forced to use conda though.

[olgOk]

Thanks! Used conda force to install. However, I had to create a separate env for the rdkit specifically.

[UnixJunkie]

Yeah, I am not surprised. Conda also is seriously lacking, and not even available as a standard system-wide package on most Linux distributions...